This may not be 100% original, this is simply what I think will happen some I've read elsewhere, some I've thought of and some I've discussed with my friends.

All of the 1st and 3rd generation dragon slayers, so not Laxus or Cobra, are from the past - hence why Natsu and Gajeel could not pass through Freed's runes during the Fighting Festival.

They all had their memories wiped, except Rogue who somehow managed to hide them along with something else in his shadow.

They all spent a significant amount of time in the spirit world frozen in time similar to the Tenrou island arc. However their ages were reversed by a powerful spirit, possibly Horoglium, seeing as I can't see his only use being transport.

Future Lucy is Zeref in disguise, and has actually been around since the beginning of the 1st grand magic games making sure eclipse isn't tampered with (not sure if thats the best way to say it), hence why Crime Socirere has felt his presence.

The story about the 10,000 dragons is an after effect of eclipse being used, maybe the door works both ways past and future, also additional dimensions, where all the dragons are.

Dragon Slayers that do not require Lacrima are born with their powers and fate brings them together with their respective dragons to learn how to control them. However they are now stuck in some kind of constant loop learning and doing everything again as time recirculates.

In previous time loops Natsu will have fought Zeref and lost, however this time something will be different, probably lucy related knowing FT, but it could be something to do with Exeeds, specifically Carla seeing something, maybe the source of her power is the Dragons, explains why Dragon Slayers and exceeds are drawn together.

Natsu will pull some massively powerful attack out of his butt in spectacular Fairy Tail fashion to beat Zeref. But not kill him, they end up friends.

The Dragon Slayers and Zeref along with Igneel, Grandine and Metalicana fight achnlogia using the thing Makarov showed Gildarts under the Guild HQ. Being given the secret by Mavis in a flashback just before he uses it.

Years later when she is just founding Fairy Tail one of the Dragons contacts Mavis, tells her the secret of Lumen Histoire and asks her to keep it hidden until the time is right, passing this on to each subsequent guildmaster of Fairy Tail.

Edit 1:No idea why the numbers are messed up they are right when I use edit, if anyone can help I will fix asap (fixed)

Edit 2: Just thought maybe time travel thing maybe where the travel sickness comes from, in the case of male dragon slayers, doesn't seem to be a problem for Wendy. But this doesn't explain Laxus.

I...hate time travel. It's like just asking for plotholes to appear, especially in long series like this that are sure to have elements forgotten (like Natsu's grabby-fire and his oh so deep bond with Macao).

It certainly would seem to make sense that the Dragon Slayers are from the past, though, given the yet unexplained reaction to the runes, and how was said in the beginning that dragon slayer magic was closer to the source magic and was lost a long time ago, and how none of them had parents. It must also tie in somehow to how all of them have transportation difficulties, since he bothered to retcon it in for the other characters.

I kinda feel like if time travel is being brought in and if these elements are coming to light that maybe the GMG arc will lead into a larger, final arc.

What if when Lucy came back to the past Cell snuck in with her and is here looking to absorb the Dragon Slayers and become Perfect since all the Dragon Slayers are gone in the future hence all the dragons.

This is probably the most accurate theory so far. I think Acnologia js actually Cell. He absorbed the power of dragons to gain power. He probably went through Eclipse and ended up further back in time.